Diego Costa stroked home the only goal of the Madrid derby as Atletico stunned Real at the Bernabeu for the second time in under five months.
The Brazilian striker scored in the 11th minute and might be disappointed to have not added to his tally, but one was enough as Atletico continued to match Barcelona stride for stride at the top of the Primera Division.
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This seventh successive win came despite Real finishing the game with both Cristiano Ronaldo and Gareth Bale, making his home debut after an B£85million move from Tottenham, on the pitch.
It may prove hugely significant come next May. On a late September evening it seemed significant enough.
Atletico, who ended a 25-match winless run against Real by beating them at the Bernabeu in last season's Copa del Rey final, had an excellent first half and deservedly led.
A game that began at a typically hectic pace took its intriguing turn when a mistake from Angel Di Maria left Madrid flat-footed and a quick pass from Koke behind the defence played in Costa.
As Madrid waited for an offside flag, Costa brought the ball under his control and guided a low 15-yard finish under Diego Lopez and across goal into the bottom right corner.
With Ronaldo quiet, it fell to Di Maria to provide the early creativity as he looked to atone for his defensive lapse. One cross from the right for Karim Benzema was made to measure, and the French striker's header might have beaten Thibaut Courtois had it not taken a touch off Diego Godin that went unnoticed by referee Antonio Mateu.
A clear chance arrived at the other end for Tiago but the only impressive part of the midfielder's attempt to head Atletico 2-0 in front was his dash to meet a right-wing corner. His unmarked header from 10 yards floated harmlessly high over the bar.
An equally good chance from an identical situation arrived in the 41st minute and Lopez made a fine double save, firstly to deny Gabi when his powerful downwards header hit the target, and then when Costa lunged in, lustily chasing the loose ball.
Real brought on Luka Modric and Bale for the second half, as Di Maria and Asier Illarramendi made way.
The Copa del Rey victory was a warning shot from Atletico to their illustrious neighbours and this reinforced their threat to the familiar Real-Barcelona duopoly in the Spanish league.
Costa scored the opener in the cup final, while Ronaldo and Gabi were sent off and Jose Mourinho banished from the touchline.
With Mourinho gone, Carlo Ancelotti is at the Real helm.
Along the touchline, Atletico boss Diego Simeone, with his oiled-back black hair and dark suit, and forthright touchline manner, cut a menacing figure throughout Saturday's game, one to whom his players were responding.
Costa raced behind the static Real defence again on the hour but fluffed his control. Despite getting a firm low shot on target, it was straight at Lopez.
At the other end, Bale went down on the edge of the penalty area. Deferring to Ronaldo, Bale watched as his new team-mate lashed the free-kick halfway up the stand behind Courtois' goal.
Ronaldo and Modric threatened with further shots on goal but Koke might have finished Real off in the 81st minute, when with his left boot he skilfully clipped a shot towards the top left corner from 15 yards, only for the crossbar to deny him.
Twenty-year-old substitute Alvaro Morata looked the most likely saviour for Real, and his acrobatic volley was well pushed away by Courtois. Tiago hit the outside of the post at one end, Morata found the sidenetting at the other.
It was Atletico's night. Increasingly they might be thinking it could be their season.